CENATAC

protein-coding

centrosomal AT-AC splicing factor

Gene summary

This gene encodes a protein thought to contain a coiled coil motif. No function has been determined for the encoded protein. A pseudogene of this gene is located on chromosome 20. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

Previous symbols:

CCDC84

MANE transcript

NM_198489.3

Inheritance

ClinVar variants

P:2U:72B:4

Top phenotype

Mosaic variegated aneuploidy syndrome 4

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr11:118,998,138-119,015,793

External References & Databases

Ensembl (ENSG00000186166)

Transcript & Mutation Effects

hg38 • Region Span ~17.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mosaic variegated aneuploidy syndrome 4LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0859329

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CENATAC variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 72

Mosaic variegated aneuploidy syndrome 4Total: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198489.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	1 clinvar		70 clinvar	4 clinvar		75
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar		1 clinvar			2
Total	2	0	72	4	0	78

Highest pathogenic variant AF is 0.000011240431

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198489.3	RefSeq	NP_940891.1	11	MANE Select
ENST00000334418.6	Ensembl	ENSP00000334767.1	11	MANE Select
ENST00000526463.5	Ensembl	ENSP00000436340.1	4	Standard
ENST00000532132.5	Ensembl	ENSP00000431889.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334418
Coding exons: 11
Length: 17650
Individuals with no LoFs: 125653
Homozygous LoFs: 0
Heterozygous LoFs: 95
Defined: 125748
p: 0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0494	186	188	0.990	0.00000928	2158
Missense (PolyPhen)		79	79.839	0.98949		874
Synonymous	1.18	53	65.1	0.814	0.00000286	599
Loss of Function	0.502	22	24.7	0.891	0.00000127	257

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00066	0.00064	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00040	0.00039	rare
South Asian	0.00027	0.00026	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.847
RVIS EVS: -0.38
RVIS percentile EVS: 27.69

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium